Package ffx.openmm

Class CMAPTorsionForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.CMAPTorsionForce
public class CMAPTorsionForce extends Force
This class implements an interaction between pairs of dihedral angles. The interaction energy is defined by an "energy correction map" (CMAP), which is simply a set of tabulated energy values on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute forces and energies at arbitrary values of the two angles.

To use this class, first create one or more energy correction maps by calling addMap(). For each one, you provide an array of energies at uniformly spaced values of the two angles. Next, add interactions by calling addTorsion(). For each one, you specify the sequence of particles used to calculate each of the two dihedral angles, and the index of the map used to calculate their interaction energy.

  • Constructor Details

    • CMAPTorsionForce

      public CMAPTorsionForce()
      Create a CMAPTorsionForce.

  • Method Details

    • addMap

      public int addMap(int size, com.sun.jna.ptr.PointerByReference energy)
      Create a new map that can be used for torsion pairs.
      Parameters:
      size - the size of the map along each dimension
      energy - the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.
      Returns:
      the index of the map that was added

    • addTorsion

      public int addTorsion(int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)
      Add a CMAP torsion term to the force field.
      Parameters:
      map - the index of the map to use for this term
      a1 - the index of the first particle forming the first torsion
      a2 - the index of the second particle forming the first torsion
      a3 - the index of the third particle forming the first torsion
      a4 - the index of the fourth particle forming the first torsion
      b1 - the index of the first particle forming the second torsion
      b2 - the index of the second particle forming the second torsion
      b3 - the index of the third particle forming the second torsion
      b4 - the index of the fourth particle forming the second torsion
      Returns:
      the index of the torsion that was added

    • destroy

      public void destroy()
      Destroy the force.
      Specified by:
      destroy in class Force

    • getMapParameters

      public void getMapParameters(int index, com.sun.jna.ptr.IntByReference size, com.sun.jna.ptr.PointerByReference energy)
      Get the energy values of a map.
      Parameters:
      index - the index of the map for which to get energy values
      size - the size of the map along each dimension
      energy - the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

    • getMapParameters

      public void getMapParameters(int index, IntBuffer size, com.sun.jna.ptr.PointerByReference energy)
      Get the energy values of a map.
      Parameters:
      index - the index of the map for which to get energy values
      size - the size of the map along each dimension
      energy - the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

    • getNumMaps

      public int getNumMaps()
      Get the number of maps that have been defined.

    • getNumTorsions

      public int getNumTorsions()
      Get the number of CMAP torsion terms in the potential function

    • getTorsionParameters

      public void getTorsionParameters(int index, com.sun.jna.ptr.IntByReference map, com.sun.jna.ptr.IntByReference a1, com.sun.jna.ptr.IntByReference a2, com.sun.jna.ptr.IntByReference a3, com.sun.jna.ptr.IntByReference a4, com.sun.jna.ptr.IntByReference b1, com.sun.jna.ptr.IntByReference b2, com.sun.jna.ptr.IntByReference b3, com.sun.jna.ptr.IntByReference b4)
      Get the force field parameters for a CMAP torsion term.
      Parameters:
      index - the index of the torsion for which to get parameters
      map - the index of the map to use for this term
      a1 - the index of the first particle forming the first torsion
      a2 - the index of the second particle forming the first torsion
      a3 - the index of the third particle forming the first torsion
      a4 - the index of the fourth particle forming the first torsion
      b1 - the index of the first particle forming the second torsion
      b2 - the index of the second particle forming the second torsion
      b3 - the index of the third particle forming the second torsion
      b4 - the index of the fourth particle forming the second torsion

    • getTorsionParameters

      public void getTorsionParameters(int index, IntBuffer map, IntBuffer a1, IntBuffer a2, IntBuffer a3, IntBuffer a4, IntBuffer b1, IntBuffer b2, IntBuffer b3, IntBuffer b4)
      Get the force field parameters for a CMAP torsion term.
      Parameters:
      index - the index of the torsion for which to get parameters
      map - the index of the map to use for this term
      a1 - the index of the first particle forming the first torsion
      a2 - the index of the second particle forming the first torsion
      a3 - the index of the third particle forming the first torsion
      a4 - the index of the fourth particle forming the first torsion
      b1 - the index of the first particle forming the second torsion
      b2 - the index of the second particle forming the second torsion
      b3 - the index of the third particle forming the second torsion
      b4 - the index of the fourth particle forming the second torsion

    • setMapParameters

      public void setMapParameters(int index, int size, com.sun.jna.ptr.PointerByReference energy)
      Set the energy values of a map.
      Parameters:
      index - the index of the map for which to set energy values
      size - the size of the map along each dimension
      energy - the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

    • setTorsionParameters

      public void setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)
      Set the force field parameters for a CMAP torsion term.
      Parameters:
      index - the index of the torsion for which to set parameters
      map - the index of the map to use for this term
      a1 - the index of the first particle forming the first torsion
      a2 - the index of the second particle forming the first torsion
      a3 - the index of the third particle forming the first torsion
      a4 - the index of the fourth particle forming the first torsion
      b1 - the index of the first particle forming the second torsion
      b2 - the index of the second particle forming the second torsion
      b3 - the index of the third particle forming the second torsion
      b4 - the index of the fourth particle forming the second torsion

    • setUsesPeriodicBoundaryConditions

      public void setUsesPeriodicBoundaryConditions(boolean periodic)
      Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

    • updateParametersInContext

      public void updateParametersInContext(Context context)
      Update the map and torsion parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

      The only information that can be updated with this method is the energy values for a map, and the map index for a torsion. The size of a map and the set of particles involved in a torsion cannot be changed. Also, new bonds and torsions cannot be added.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Returns whether or not this force makes use of periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      true if force uses PBC and false otherwise